So after a quick google, it seems to confirm that windows based software is not touching the bios, correct?
Maybe that might be made a little more clear if we said that software used from within the operating system is not writing any changes to the firmware programmed onto the bios chip nor that made by users and "saved" to CMOS.
However the software used within windows is over-riding information from the bios, given to the system setup done at booting.
RGone...
EDIT:
Let me make a small addition here from one without sheepskin of any type. Nothing about a computer is just done in thin air. It is stored or located somewhere. One of the reasons that ram is checked near the beginning of booting is that the bios information is expanded into ram. You all remember and still think many bioses have the option to use a "shadow ram" menu item which kept the bios information in ram after bootup. Many of us would disable that to allow more space in the ram.
Now we come to software that is changing the system running parameters. Is additional space taken up by the software in ram? I have not found any answer directly to this. Might take someone smarter than me to just "know" how that circumstance might be answered.
I guess where I am going is here. If a setting must be re-polled, the bios has not changed nor is corrupt so the RE-poll gets an accurate answer. However if the bios is being over-ridden by software and there is a RE-poll of specific settings the setting is now coming from software that can be being corrrupted in the O/S or Ram.
I knew when this particular conversation was pursued that there would be some dead-ends. Software for overclocking can be pretty proprietary. Or maybe not, but the full disclosure will likely not be forthcoming as to all that the software can do or how it does it. And I fear in the end it will be a subject that will not have a full and complete answer or understanding.
No full understanding is why I will continue to overclock from the Bios itself until I decide I want to try for that last few MHZ that are not stable enough to allow the operating system to boot as it normally would and should. After reaching that super MHZ, I will continue to unload the software overclocking tool and go back to business as usual. That is me though.
END EDIT.